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Wang Z, Cui T, Wang Q. Optimization of degradation conditions and analysis of degradation mechanism for nitrite by Bacillus aryabhattai 47. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171096. [PMID: 38387569 DOI: 10.1016/j.scitotenv.2024.171096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/17/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Excessive nitrite levels cause significant damage to aquaculture, making it crucial to explore green and reliable nitrite removal technologies. In this study, A Bacillus aryabhattai (designated as the strain 47) isolated from aquaculture wastewater was used as the experimental strain. The nitrite degradation conditions of the strain 47 were optimized, and the optimal conditions are: glucose was 12.74 g/L, fermented special soybean meal was 21.27 g/L, MgCl2 369 mg/L, pH 7.0, incubated at 30 °C with the inoculum size of 2 % and the rotation speed of 170 rpm. Under the optimal conditions, the nitrite concentration of the culture solution was 200 mg/L, and the nitrite removal rate reached 91.4 %. Meanwhile, the mechanism by which Mg2+ enhanced the nitrite degradation ability of the strain 47 was investigated by transcriptomics. An operon structure directed cellular trafficking of Mg2+, and then, the Mg2+-mediated catalytic reaction of multiple enzymes enhanced and improved cellular metabolic processes (e.g. the transport and metabolism of nitrite, central carbohydrate metabolism oxidative phosphorylation). At the same time, with the progress of cell metabolism, cells secreted a series of enzymes related to nitrite transport and metabolism to promote the metabolism of nitrite. And the process of the assimilated nitrate reduction pathway of nitrite degradation in the strain 47 was elaborated at the transcriptome level. This study provided a new insight into nitrite treatment mediated by microbial organisms.
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Affiliation(s)
- Zhenhao Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Tangbing Cui
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
| | - Qiang Wang
- Guangdong Yuzanchen Biotechnology Co., Ltd, Jiangmen 529100, PR China
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Chen W, Ji G, Wu R, Fang C, Lu H. Mass spectrometry-based candidate substrate and site identification of PTM enzymes. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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Elucidation of the interaction proteome of mitochondrial chaperone Hsp78 highlights its role in protein aggregation during heat stress. J Biol Chem 2022; 298:102494. [PMID: 36115461 PMCID: PMC9574514 DOI: 10.1016/j.jbc.2022.102494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Chaperones of the Hsp100/Clp family represent major components of protein homeostasis, conferring maintenance of protein activity under stress. The ClpB-type members of the family, present in bacteria, fungi, and plants, are able to resolubilize aggregated proteins. The mitochondrial member of the ClpB family in Saccharomyces cerevisiae is Hsp78. Although Hsp78 has been shown to contribute to proteostasis in elevated temperatures, the biochemical mechanisms underlying this mitochondria-specific thermotolerance are still largely unclear. To identify endogenous chaperone substrate proteins, here, we generated an Hsp78-ATPase mutant with stabilized substrate-binding behavior. We used two stable isotope labeling–based quantitative mass spectrometry approaches to analyze the role of Hsp78 during heat stress–induced mitochondrial protein aggregation and disaggregation on a proteomic level. We first identified the endogenous substrate spectrum of the Hsp78 chaperone, comprising a wide variety of proteins related to metabolic functions including energy production and protein synthesis, as well as other chaperones, indicating its crucial functions in mitochondrial stress resistance. We then compared these interaction data with aggregation and disaggregation processes in mitochondria under heat stress, which revealed specific aggregation-prone protein populations and demonstrated the direct quantitative impact of Hsp78 on stress-dependent protein solubility under different conditions. We conclude that Hsp78, together with its cofactors, represents a recovery system that protects major mitochondrial metabolic functions during heat stress as well as restores protein biogenesis capacity after the return to normal conditions.
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Hsp100 Molecular Chaperone ClpB and Its Role in Virulence of Bacterial Pathogens. Int J Mol Sci 2021; 22:ijms22105319. [PMID: 34070174 PMCID: PMC8158500 DOI: 10.3390/ijms22105319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 01/05/2023] Open
Abstract
This review focuses on the molecular chaperone ClpB that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and its biological function in selected bacterial pathogens, causing a variety of human infectious diseases, including zoonoses. It has been established that ClpB disaggregates and reactivates aggregated cellular proteins. It has been postulated that ClpB’s protein disaggregation activity supports the survival of pathogenic bacteria under host-induced stresses (e.g., high temperature and oxidative stress), which allows them to rapidly adapt to the human host and establish infection. Interestingly, ClpB may also perform other functions in pathogenic bacteria, which are required for their virulence. Since ClpB is not found in human cells, this chaperone emerges as an attractive target for novel antimicrobial therapies in combating bacterial infections.
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Functional Expression, Purification and Identification of Interaction Partners of PACRG. Molecules 2021; 26:molecules26082308. [PMID: 33923444 PMCID: PMC8074078 DOI: 10.3390/molecules26082308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
PACRG (Parkin co-regulated gene) shares a bi-directional promoter with the Parkinson’s disease-associated gene Parkin, but the physiological roles of PACRG have not yet been fully elucidated. Recombinant expression methods are indispensable for protein structural and functional studies. In this study, the coding region of PACRG was cloned to a conventional vector pQE80L, as well as two cold-shock vectors pCold II and pCold-GST, respectively. The constructs were transformed into Escherichia coli (DE3), and the target proteins were overexpressed. The results showed that the cold-shock vectors are more suitable for PACRG expression. The soluble recombinant proteins were purified with Ni2+ chelating column, glutathione S-transferase (GST) affinity chromatography and gel filtration. His6 pull down assay and LC-MS/MS were carried out for identification of PACRG-binding proteins in HEK293T cell lysates, and a total number of 74 proteins were identified as potential interaction partners of PACRG. GO (Gene ontology) enrichment analysis (FunRich) of the 74 proteins revealed multiple molecular functions and biological processes. The highest proportion of the 74 proteins functioned as transcription regulator and transcription factor activity, suggesting that PACRG may play important roles in regulation of gene transcription.
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AAA+ Molecular Chaperone ClpB in Leptospira interrogans: Its Role and Significance in Leptospiral Virulence and Pathogenesis of Leptospirosis. Int J Mol Sci 2020; 21:ijms21186645. [PMID: 32932775 PMCID: PMC7555560 DOI: 10.3390/ijms21186645] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial ClpB is an ATP-dependent disaggregase that belongs to the Hsp100/Clp subfamily of the AAA+ ATPases and cooperates with the DnaK chaperone system in the reactivation of aggregated proteins, as well as promotes bacterial survival under adverse environmental conditions, including thermal and oxidative stresses. In addition, extensive evidence indicates that ClpB supports the virulence of numerous bacteria, including pathogenic spirochaete Leptospira interrogans responsible for leptospirosis in animals and humans. However, the specific function of ClpB in leptospiral virulence still remains to be fully elucidated. Interestingly, ClpB was predicted as one of the L. interrogans hub proteins interacting with human proteins, and pathogen–host protein interactions are fundamental for successful invasion of the host immune system by bacteria. The aim of this review is to discuss the most important aspects of ClpB’s function in L. interrogans, including contribution of ClpB to leptospiral virulence and pathogenesis of leptospirosis, a zoonotic disease with a significant impact on public health worldwide.
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of ClpB From Corynebacterium crenatum in Thermal Stress and Arginine Fermentation. Front Microbiol 2020; 11:1660. [PMID: 32765470 PMCID: PMC7380099 DOI: 10.3389/fmicb.2020.01660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/25/2020] [Indexed: 12/04/2022] Open
Abstract
ClpB, an ATP-dependent molecular chaperone, is involved in metabolic pathways and plays important roles in microorganisms under stress conditions. Metabolic pathways and stress resistance are important characteristics of industrially -relevant bacteria during fermentation. Nevertheless, ClpB-related observations have been rarely reported in industrially -relevant microorganisms. Herein, we found a homolog of ClpB from Corynebacterium crenatum. The amino acid sequence of ClpB was analyzed, and the recombinant ClpB protein was purified and characterized. The full function of ClpB requires DnaK as chaperone protein. For this reason, dnaK/clpB deletion mutants and the complemented strains were constructed to investigate the role of ClpB. The results showed that DnaK/ClpB is not essential for the survival of C. crenatum MT under pH and alcohol stresses. The ClpB-deficient or DnaK-deficient C. crenatum mutants showed weakened growth during thermal stress. In addition, the results demonstrated that deletion of the clpB gene affected glucose consumption and L-arginine, L-glutamate, and lactate production during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, Nanchang, China
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Kędzierska-Mieszkowska S, Potrykus K, Arent Z, Krajewska J. Identification of σ E-Dependent Promoter Upstream of clpB from the Pathogenic Spirochaete Leptospira interrogans by Applying an E. coli Two-Plasmid System. Int J Mol Sci 2019; 20:ijms20246325. [PMID: 31847479 PMCID: PMC6941012 DOI: 10.3390/ijms20246325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 11/16/2022] Open
Abstract
There is limited information on gene expression in the pathogenic spirochaete Leptospira interrogans and genetic mechanisms controlling its virulence. Transcription is the first step in gene expression that is often determined by environmental effects, including infection-induced stresses. Alterations in the environment result in significant changes in the transcription of many genes, allowing effective adaptation of Leptospira to mammalian hosts. Thus, promoter and transcriptional start site identification are crucial for determining gene expression regulation and for the understanding of genetic regulatory mechanisms existing in Leptospira. Here, we characterized the promoter region of the L. interrogans clpB gene (clpBLi) encoding an AAA+ molecular chaperone ClpB essential for the survival of this spirochaete under thermal and oxidative stresses, and also during infection of the host. Primer extension analysis demonstrated that transcription of clpB in L. interrogans initiates at a cytidine located 41 bp upstream of the ATG initiation codon, and, to a lesser extent, at an adenine located 2 bp downstream of the identified site. Transcription of both transcripts was heat-inducible. Determination of clpBLi transcription start site, combined with promoter transcriptional activity assays using a modified two-plasmid system in E. coli, revealed that clpBLi transcription is controlled by the ECF σE factor. Of the ten L. interrogans ECF σ factors, the factor encoded by LIC_12757 (LA0876) is most likely to be the key regulator of clpB gene expression in Leptospira cells, especially under thermal stress. Furthermore, clpB expression may be mediated by ppGpp in Leptospira.
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Affiliation(s)
- Sabina Kędzierska-Mieszkowska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, 80-308 Gdańsk, Poland;
- Correspondence: ; Tel./Fax: +48-58-523-6064
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland;
| | - Zbigniew Arent
- University Centre of Veterinary Medicine, University of Agriculture in Krakow, 30-059 Krakow, Poland;
| | - Joanna Krajewska
- Department of General and Medical Biochemistry, University of Gdańsk, Faculty of Biology, 80-308 Gdańsk, Poland;
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Montandon C, Friso G, Liao JYR, Choi J, van Wijk KJ. In Vivo Trapping of Proteins Interacting with the Chloroplast CLPC1 Chaperone: Potential Substrates and Adaptors. J Proteome Res 2019; 18:2585-2600. [DOI: 10.1021/acs.jproteome.9b00112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cyrille Montandon
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Junsik Choi
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
| | - Klaas J. van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York 14853, United States
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Rei Liao JY, van Wijk KJ. Discovery of AAA+ Protease Substrates through Trapping Approaches. Trends Biochem Sci 2019; 44:528-545. [PMID: 30773324 DOI: 10.1016/j.tibs.2018.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022]
Abstract
Proteases play essential roles in cellular proteostasis. Mechanisms through which proteases recognize their substrates are often hard to predict and therefore require experimentation. In vivo trapping allows systematic identification of potential substrates of proteases, their adaptors, and chaperones. This combines in vivo genetic modifications of proteolytic systems, stabilized protease-substrate interactions, affinity enrichments of trapped substrates, and mass spectrometry (MS)-based identification. In vitro approaches, in which immobilized protease components are incubated with isolated cellular proteome, complement this in vivo approach. Both approaches can provide information about substrate recognition signals, degrons, and conditional effects. This review summarizes published trapping studies and their biological outcomes, and provides recommendations for substrate trapping of the processive AAA+ Clp, Lon, and FtsH chaperone proteolytic systems.
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Affiliation(s)
- Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA.
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Kumar S, Lata KS, Sharma P, Bhairappanavar SB, Soni S, Das J. Inferring pathogen-host interactions between Leptospira interrogans and Homo sapiens using network theory. Sci Rep 2019; 9:1434. [PMID: 30723266 PMCID: PMC6363727 DOI: 10.1038/s41598-018-38329-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/20/2018] [Indexed: 12/19/2022] Open
Abstract
Leptospirosis is the most emerging zoonotic disease of epidemic potential caused by pathogenic species of Leptospira. The bacterium invades the host system and causes the disease by interacting with the host proteins. Analyzing these pathogen-host protein interactions (PHPIs) may provide deeper insight into the disease pathogenesis. For this analysis, inter-species as well as intra-species protein interactions networks of Leptospira interrogans and human were constructed and investigated. The topological analyses of these networks showed lesser connectivity in inter-species network than intra-species, indicating the perturbed nature of the inter-species network. Hence, it can be one of the reasons behind the disease development. A total of 35 out of 586 PHPIs were identified as key interactions based on their sub-cellular localization. Two outer membrane proteins (GpsA and MetXA) and two periplasmic proteins (Flab and GlyA) participating in PHPIs were found conserved in all pathogenic, intermediate and saprophytic spp. of Leptospira. Furthermore, the bacterial membrane proteins involved in PHPIs were found playing major roles in disruption of the immune systems and metabolic processes within host and thereby causing infectious disease. Thus, the present results signify that the membrane proteins participating in such interactions hold potential to serve as effective immunotherapeutic candidates for vaccine development.
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Affiliation(s)
- Swapnil Kumar
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Kumari Snehkant Lata
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Priyanka Sharma
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Shivarudrappa B Bhairappanavar
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Subhash Soni
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India
| | - Jayashankar Das
- Gujarat Biotechnology Research Centre, Department of Science & Technology, Government of Gujarat, Gandhinagar, 382011, India.
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Vinaiphat A, Thongboonkerd V. Chaperonomics in leptospirosis. Expert Rev Proteomics 2018; 15:569-579. [PMID: 30004813 DOI: 10.1080/14789450.2018.1500901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Knowledge of the function of molecular chaperones is required for a better understanding of cellular proteostasis. Nevertheless, such information is currently dispersed as most of previous studies investigated chaperones on a single-angle basis. Recently, a new subdiscipline of chaperonology, namely 'chaperonomics' (defined as 'systematic analysis of chaperone genes, transcripts, proteins, or their interaction networks using omics technologies'), has been emerging to better understand biological, physiological, and pathological roles of chaperones. Areas covered: This review provides broad overviews of bacterial chaperones, heat shock proteins (HSPs), and leptospirosis, and then focuses on recent progress of chaperonomics applied to define roles of HSPs in various pathogenic and saprophytic leptospiral species and serovars. Expert commentary: Comprehensive analysis of leptospiral chaperones/HSPs using a chaperonomics approach holds great promise for better understanding of functional roles of chaperones/HSPs in bacterial survival and disease pathogenesis. Moreover, this new approach may also lead to further development of chaperones/HSPs-based diagnostics and/or vaccine discovery for leptospirosis.
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Affiliation(s)
- Arada Vinaiphat
- a Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Visith Thongboonkerd
- a Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
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